Zinc in PDB 6r55: Crystal Structure of Ppep-1(E184K)

All present enzymatic activity of Crystal Structure of Ppep-1(E184K):
3.4.24.89;

The structure of Crystal Structure of Ppep-1(E184K), PDB code: 6r55 was solved by C.Pichlo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.51 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.970, 71.670, 117.810, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.3

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(E184K) (pdb code 6r55). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Ppep-1(E184K), PDB code: 6r55:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ppep-1(E184K)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ppep-1(E184K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:13.7 occ:1.00 OE1 A:GLU185 2.1 12.0 1.0 O2 A:TRS301 2.1 12.8 1.0 NE2 A:HIS142 2.1 9.8 1.0 N A:TRS301 2.1 13.4 1.0 NE2 A:HIS146 2.1 12.8 1.0 O3 A:TRS301 2.1 14.0 1.0 HN2 A:TRS301 2.3 16.1 1.0 C A:TRS301 2.8 13.7 1.0 HN1 A:TRS301 2.8 16.1 1.0 C3 A:TRS301 2.9 14.2 1.0 C2 A:TRS301 2.9 13.0 1.0 CD A:GLU185 3.0 15.4 1.0 CD2 A:HIS142 3.0 11.8 1.0 CE1 A:HIS146 3.1 13.3 1.0 CD2 A:HIS146 3.1 11.9 1.0 CE1 A:HIS142 3.1 11.2 1.0 HD2 A:HIS142 3.1 14.1 1.0 OE2 A:GLU185 3.2 14.3 1.0 HE1 A:HIS146 3.3 16.0 1.0 HD2 A:HIS146 3.3 14.3 1.0 HE1 A:HIS142 3.4 13.4 1.0 H31 A:TRS301 3.4 17.1 1.0 H22 A:TRS301 3.6 15.6 1.0 H21 A:TRS301 3.7 15.6 1.0 H32 A:TRS301 3.8 17.1 1.0 O A:HOH523 4.1 16.1 1.0 CG A:HIS142 4.2 9.5 1.0 HA A:GLU185 4.2 13.9 1.0 ND1 A:HIS146 4.2 11.9 1.0 ND1 A:HIS142 4.2 11.9 1.0 OE2 A:GLU143 4.2 13.5 1.0 CG A:HIS146 4.2 11.2 1.0 C1 A:TRS301 4.2 14.6 1.0 OH A:TYR178 4.3 16.8 1.0 O A:HOH579 4.4 13.6 1.0 HB3 A:ALA188 4.4 14.0 1.0 CG A:GLU185 4.4 13.2 1.0 HB3 A:GLU185 4.6 11.5 1.0 HE3 A:LYS184 4.6 52.7 1.0 H11 A:TRS301 4.6 17.5 1.0 HE2 A:TYR178 4.6 15.2 1.0 HH A:TYR178 4.7 20.1 1.0 HG3 A:GLU185 4.8 15.9 1.0 HO1 A:TRS301 4.8 18.4 1.0 HB1 A:ALA188 4.9 14.0 1.0 O1 A:TRS301 4.9 15.3 1.0 CB A:GLU185 4.9 9.6 1.0 H12 A:TRS301 4.9 17.5 1.0 OE1 A:GLU143 4.9 16.8 1.0 HZ1 A:LYS101 5.0 49.1 1.0 HE2 A:LYS184 5.0 52.7 1.0 HD1 A:HIS146 5.0 14.3 1.0 CB A:ALA188 5.0 11.7 1.0 CD A:GLU143 5.0 11.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(E184K)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ppep-1(E184K) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:12.0 occ:1.00 NE2 B:HIS142 2.1 8.7 1.0 N B:TRS301 2.1 11.3 1.0 NE2 B:HIS146 2.1 8.8 1.0 OE1 B:GLU185 2.1 11.6 1.0 O2 B:TRS301 2.1 11.3 1.0 O3 B:TRS301 2.1 11.3 1.0 HN2 B:TRS301 2.2 13.6 1.0 C B:TRS301 2.8 11.4 1.0 HN1 B:TRS301 2.8 13.6 1.0 C3 B:TRS301 2.9 10.8 1.0 C2 B:TRS301 2.9 11.7 1.0 CD2 B:HIS142 3.0 9.1 1.0 CD B:GLU185 3.0 12.1 1.0 CD2 B:HIS146 3.1 11.2 1.0 CE1 B:HIS146 3.1 10.5 1.0 CE1 B:HIS142 3.1 11.3 1.0 HD2 B:HIS142 3.2 10.9 1.0 HD2 B:HIS146 3.2 13.5 1.0 OE2 B:GLU185 3.3 12.2 1.0 HE1 B:HIS146 3.3 12.6 1.0 HE1 B:HIS142 3.3 13.6 1.0 H31 B:TRS301 3.4 12.9 1.0 H22 B:TRS301 3.6 14.0 1.0 H21 B:TRS301 3.7 14.0 1.0 H32 B:TRS301 3.8 12.9 1.0 O B:HOH551 4.2 14.0 1.0 OE2 B:GLU143 4.2 13.4 1.0 CG B:HIS142 4.2 9.7 1.0 ND1 B:HIS142 4.2 10.8 1.0 HA B:GLU185 4.2 11.5 1.0 ND1 B:HIS146 4.2 10.7 1.0 CG B:HIS146 4.2 10.8 1.0 C1 B:TRS301 4.2 12.0 1.0 OH B:TYR178 4.3 12.9 1.0 O B:HOH594 4.4 12.2 1.0 HB3 B:ALA188 4.4 15.1 1.0 CG B:GLU185 4.4 11.0 1.0 HB3 B:GLU185 4.5 10.7 1.0 H11 B:TRS301 4.6 14.4 1.0 HE2 B:TYR178 4.6 14.2 1.0 HE3 B:LYS184 4.6 32.7 1.0 HH B:TYR178 4.7 15.5 1.0 HG3 B:GLU185 4.8 13.2 1.0 HB1 B:ALA188 4.8 15.1 1.0 OE1 B:GLU143 4.8 13.5 1.0 O1 B:TRS301 4.8 12.1 1.0 CB B:GLU185 4.9 8.9 1.0 H12 B:TRS301 4.9 14.4 1.0 CD B:GLU143 4.9 15.7 1.0 CB B:ALA188 4.9 12.6 1.0 HB2 B:ALA188 4.9 15.1 1.0 HD1 B:HIS142 5.0 12.9 1.0 HD1 B:HIS146 5.0 12.8 1.0 CA B:GLU185 5.0 9.6 1.0

C.Pichlo, L.Juetten, F.Wojtalla, M.Schacherl, D.Diaz, U.Baumann. Molecular Determinants of the Mechanism and Substrate Specificity Ofclostridium Difficileproline-Proline Endopeptidase-1. J.Biol.Chem. V. 294 11525 2019.
ISSN: ESSN 1083-351X
PubMed: 31182482
DOI: 10.1074/JBC.RA119.009029